Understanding the interactions between bacteria in the human gut through metabolic modeling
Journal article, 2013

The human gut microbiome plays an influential role in maintaining human health, and it is a potential target for prevention and treatment of disease. Genome-scale metabolic models (GEMs) can provide an increased understanding of the mechanisms behind the effects of diet, the genotype-phenotype relationship and microbial robustness. Here we reconstructed GEMs for three key species, (Bacteroides thetaiotamicron, Eubacterium rectale and Methanobrevibacter smithii) as relevant representatives of three main phyla in the human gut (Bacteroidetes, Firmicutes and Euryarchaeota). We simulated the interactions between these three bacteria in different combinations of gut ecosystems and compared the predictions with the experimental results obtained from colonization of germ free mice. Furthermore, we used our GEMs for analyzing the contribution of each species to the overall metabolism of the gut microbiota based on transcriptome data and demonstrated that these models can be used as a scaffold for understanding bacterial interactions in the gut.

MUTUALISM

HEALTH

METHANOBREVIBACTER-SMITHII

NETWORK

LARGE-INTESTINE

HUMAN COLONIC MICROBIOTA

METAGENOME

ABSORPTION

BUTYRATE

DIET

Author

Saeed Shoaie

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

Fredrik Karlsson

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

Adil Mardinoglu

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

Intawat Nookaew

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

Sergio Velasco

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

Jens B Nielsen

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

Scientific Reports

2045-2322 (ISSN)

Vol. 3 2532

Infrastructure

C3SE (Chalmers Centre for Computational Science and Engineering)

Subject Categories

Other Natural Sciences

DOI

10.1038/srep02532

More information

Created

10/7/2017